Godzilla VS King Ghidorah has a signifigant hidden depth to it. However without historical context and knowledge of the events leading up and during World War 2, it would fly over your head like King Ghidorah does.
This film has some controversy. Japanese nationalism and ethnocentrism is all over this movie, and is done so in a film where Japanese World War 2 veterans are in leadership positions and called "The men who rebuilt Japan's economy". And thanks to the time travelers, we know that this economy grows unabated into an Economic Super Power that dominates the world.
23rd century global jealousy of Japan is a major plot driving force, so it is not easy to overlook this controversy in this film. What does it mean to say Japan purchased Africa and South America? The movie doesn't explore that so we are left to our own imagination. The concept of purchasing Africa is not morally sound. The African Slave Trade is a shameful part of American history, just as the events before and during World War 2 are shameful for Japan. That comparison is made because this movie is talking about both in utero.
The path that Shindo has set for his country in years after World War 2 at first glance seems like an unbridled success. But thanks to successive time traveling events, that same path also erases Japan from the timeline, until other time traveling shenanigans again find a way to save Japan, but also make it a normal part of the Earth civilization instead of completely dominating it.
Shindo has a relationship with Godzilla that in many ways parallel Moby Dick. Shindo personifies a proto-Godzilla's accidental protection as altruistic, only to be disappointed when Godzilla is in fact a come one come all humanity destroyer.
Shindo's sadness and willingness to die reflects several key points. Shindo acknowledges that the path Japan is on is wrong, and he is willing to step aside to let new leaders forge a new direction. The success he's enjoyed since World War 2 does not absolve the horrors he may have even participated in during said war.
The larger picture of Shindo allowing himself to die is one of true existential horror — how could this be us? Some soldiers were good, many were not, and that is the dark demeanor Shindo wears as he sees Godzilla's inexorable approach. "I defended Japan, Godzilla defended me, Godzilla is evil, what am I?"
It is only through historical knowledge that a person could catch these messages; so these messages go right over the head of the young viewers. That is fine, children do love Godzilla and there is no reason to show them the true horrors of war and war crimes.
Shindo's leadership post World War 2 and into the future as shown us by time travelers, suggest that Shindo's Japan was still comfortable with nationalism and aggression, this time carried out by money (Japan's globally dominant economy) rather than guns (Imperial Japan's army). Shindo realizes that the future he is forging is beset by time traveling terrorists. He realizes that for a Japan that is future-proof, Japan needs to be cooperative, not hegemonic. His path is towards hegemony, but that way leads to incalculable deaths. So he allows himself to die so that the hegemonic Japan of the future will not exist as it does in the first future, which also prevents the second future where Japan does not exist at all.
At the end of the movie, the time traveler returns to what is now the third future, one the audience never learns anything about. But we do know Japan does not dominate the world, and that Japan does exist. Japan rejects the pursuit of absolute power and seeks a cooperative relationship with the rest of Earth — after all, were it not for the rest of the Earth in the 23rd century banding together to make Mecha King Ghidorah, Japan would not exist at all.
There is controversy in this movie — Japanese Nationalism is on full display at times. There is no anti-Americanism; if anything Americans are depicted as very kind and affable. The white people antagonists are clearly transnationalists with no ties to current states — and the dialog gives away that they are actually radical terrorists, not representing any state. This movie ultimately heavily criticizes Japanese Nationalism, thus Japanese Nationalism was included, and Japanese Nationalism is what is controversial.
